Pau Badia-i-Mompel
| Snapshot Date: 2026-04-03 13:45 -0400 (Fri, 03 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: RELEASE_3_22 |
| git_last_commit: ff3aa1d |
| git_last_commit_date: 2025-10-29 11:09:41 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-04 11:57 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 541/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.16.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| See other builds for decoupleR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz |
| StartedAt: 2026-04-03 22:38:35 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 22:51:02 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 746.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2026-04-03 22:39:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:39:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:39:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-03 22:39:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-03
[2026-04-03 22:39:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-04-03 19:07:52 UTC; unix
[2026-04-03 22:39:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-04-03 22:39:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-04-03 22:39:09] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-03 22:39:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-03 22:39:10] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2026-04-03); AnnotationDbi 1.72.0(2026-04-03); AUCell 1.32.0(2026-04-03); backports 1.5.1(2026-04-03); beachmat 2.26.0(2026-04-03); Biobase 2.70.0(2026-04-03); BiocGenerics 0.56.0(2026-04-03); BiocParallel 1.44.0(2026-04-03); BiocSingular 1.26.1(2026-04-03); Biostrings 2.78.0(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-04-03); DelayedArray 0.36.1(2026-04-03); DelayedMatrixStats 1.32.0(2026-04-03); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); GenomicRanges 1.62.1(2026-04-03); glue 1.8.0(2024-09-30); graph 1.88.1(2026-04-03); GSEABase 1.72.0(2026-04-03); GSVA 2.4.8(2026-04-03); h5mread 1.2.1(2026-04-03); HDF5Array 1.38.0(2026-04-03); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); IRanges 2.44.0(2026-04-03); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2026-04-03); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.22.0(2026-04-03); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); OmnipathR 3.18.4(2026-04-03); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); processx 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.54.1(2026-04-03); rhdf5filters 1.22.0(2026-04-03); Rhdf5lib 1.32.0(2026-04-03); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-04-03); S4Vectors 0.48.0(2026-04-03); ScaledMatrix 1.18.0(2026-04-03); Seqinfo 1.0.0(2026-04-03); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2026-04-03); SparseArray 1.10.10(2026-04-03); sparseMatrixStats 1.22.0(2026-04-03); SpatialExperiment 1.20.0(2026-04-03); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-04-03); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-04-03); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-03 22:39:10] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Contains 9 files.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-03 22:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-03 22:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-03 22:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-03 22:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:39:10] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_collectri 30.818 2.698 40.031
get_dorothea 23.099 1.302 26.017
run_fgsea 23.178 0.797 23.943
run_aucell 9.119 2.418 11.457
get_progeny 7.394 0.877 14.329
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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Warning: stack imbalance in '.Call', 162 then 164
[2026-04-03 22:42:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:42:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-03 22:42:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-03
[2026-04-03 22:42:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-04-03 19:07:52 UTC; unix
[2026-04-03 22:42:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-04-03 22:42:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-04-03 22:42:46] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-03 22:42:46] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-03 22:42:47] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2026-04-03); AnnotationDbi 1.72.0(2026-04-03); AUCell 1.32.0(2026-04-03); backports 1.5.1(2026-04-03); beachmat 2.26.0(2026-04-03); Biobase 2.70.0(2026-04-03); BiocGenerics 0.56.0(2026-04-03); BiocParallel 1.44.0(2026-04-03); BiocSingular 1.26.1(2026-04-03); Biostrings 2.78.0(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); broom 1.0.12(2026-01-27); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-04-03); DelayedArray 0.36.1(2026-04-03); DelayedMatrixStats 1.32.0(2026-04-03); desc 1.4.3(2023-12-10); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); e1071 1.7-17(2025-12-18); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-04-03); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); GenomicRanges 1.62.1(2026-04-03); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); graph 1.88.1(2026-04-03); GSEABase 1.72.0(2026-04-03); GSVA 2.4.8(2026-04-03); gtable 0.3.6(2024-10-25); h5mread 1.2.1(2026-04-03); HDF5Array 1.38.0(2026-04-03); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); IRanges 2.44.0(2026-04-03); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2026-04-03); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.22.0(2026-04-03); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); mixtools 2.0.0.1(2025-03-08); nlme 3.1-169(2026-03-27); OmnipathR 3.18.4(2026-04-03); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-29(2025-12-29); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.18.0(2026-01-16); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.54.1(2026-04-03); rhdf5filters 1.22.0(2026-04-03); Rhdf5lib 1.32.0(2026-04-03); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); rpart 4.1.27(2026-03-27); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-04-03); S4Vectors 0.48.0(2026-04-03); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2026-04-03); scales 1.4.0(2025-04-24); segmented 2.2-1(2026-01-29); Seqinfo 1.0.0(2026-04-03); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2026-04-03); SparseArray 1.10.10(2026-04-03); sparseMatrixStats 1.22.0(2026-04-03); SpatialExperiment 1.20.0(2026-04-03); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-04-03); survival 3.8-6(2026-01-16); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); viper 1.44.0(2026-04-03); viridisLite 0.4.3(2026-02-04); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-04-03); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-03 22:42:47] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Contains 9 files.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-03 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-03 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-03 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-03 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-04-03 22:42:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:42:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:49] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:49] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:49] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-04-03 22:42:49] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-04-03 22:42:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-03 22:42:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:42:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-03 22:42:49] [TRACE] [OmnipathR] Sending HTTP request.
[2026-04-03 22:42:50] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-04-03 22:42:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:42:50] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.626856s from rescued.omnipathdb.org (63.6 Kb/s); Redirect: 0s, DNS look up: 0.002632s, Connection: 0.003486s, Pretransfer: 0.338787s, First byte at: 0.487609s
[2026-04-03 22:42:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:42:50 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 04 Apr 2026 03:42:50 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-04-03 22:42:50] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 04 Apr 2026 02:42:50 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 04 Apr 2026 03:42:50 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-04-03 22:42:51] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-04-03 22:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:51] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-03 22:42:52] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-03 22:42:52] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-04-03 22:42:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:42:52] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-03 22:42:52] [TRACE] [OmnipathR] Downloaded 5.3 Kb in 0.208563s from omabrowser.org (25.6 Kb/s); Redirect: 0s, DNS look up: 0.000921s, Connection: 0.014204s, Pretransfer: 0.080663s, First byte at: 0.208375s
[2026-04-03 22:42:52] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 04 Apr 2026 02:42:52 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=lkv8KAzUvr0arh2r%2FFWbHp3FoFKDGMZ4fAjNjCV8Ve50GlFhouxGmb9qlIuLapnLq%2FnJ00oHqkUJ0bUbbZRrdyJdwRr6wWAifKhGuz9NSs%2FXKPRF%2FyT3R%2BXb965NqLp0BQ%3D%3D"}]}; cf-ray: 9e6cf654fa2c07df-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-03 22:42:54] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:54] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-03 22:42:54] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:42:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:42:54] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-03 22:42:54] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-03 22:42:54] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-03 22:43:25] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-03 22:43:25] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-04-03 22:43:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:25] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-04-03 22:43:25] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-04-03 22:43:26] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:43:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2026-04-03 22:43:26] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:43:26] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:43:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:43:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:43:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:43:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:43:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.341564s from omnipathdb.org (46 Kb/s); Redirect: 0s, DNS look up: 0.001909s, Connection: 0.002822s, Pretransfer: 0.195704s, First byte at: 0.340887s
[2026-04-03 22:43:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:43:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:43:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:43:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:28] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-03 22:43:28] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:28] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2026-04-03 22:43:28] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-04-03 22:43:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:43:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-03 22:43:29] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:43:29] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:43:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:43:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:43:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:43:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:43:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.355695s from omnipathdb.org (44.1 Kb/s); Redirect: 0s, DNS look up: 0.00193s, Connection: 0.00271s, Pretransfer: 0.208307s, First byte at: 0.354696s
[2026-04-03 22:43:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:43:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:43:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:43:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:38] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:43:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-03 22:43:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-03 22:43:41] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-04-03 22:43:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:41] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-04-03 22:43:41] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2026-04-03 22:43:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:43:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:43:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-03 22:43:43] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:43:43] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:43:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-03 22:43:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-03 22:43:45] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2026-04-03 22:43:46] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-03 22:43:46] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:43:47] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:43:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-03 22:43:47] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-03 22:43:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-03 22:43:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:43:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:43:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:43:58] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-03 22:43:58] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 11.385222s from omabrowser.org (1.1 Kb/s); Redirect: 0s, DNS look up: 0.000913s, Connection: 0.013813s, Pretransfer: 0.084577s, First byte at: 11.385112s
[2026-04-03 22:43:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 04 Apr 2026 02:43:58 GMT; content-type: text/tsv; charset=utf-8; content-length: 1187278; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2026-04-04_024357.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=8244793c6b91d491; expires=Mon, 03-Apr-2028 02:43:58 UTC; Path=/; cf-cache-status: DYNAMIC; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=VqOf3F5jDOYuFYykjOqjdvXMneTRy9T%2FjNKzyhBj6EFQxgtZZiZf2jbf38%2BuoWPcP0qLKBPSLw5U7%2B1BZp3wLDE4hW49lhBDPzbEI3C9MGBCwg%2BzK2bnXZdkT%2BB4qRCJ6w%3D%3D"}]}; cf-ray: 9e6cf7ab8faf14bc-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-03 22:44:00] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:00] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-03 22:44:00] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:00] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-03 22:44:00] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-03 22:44:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:44:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:44:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:44:01] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-03 22:44:01] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.801647s from rest.uniprot.org (38 bytes/s); Redirect: 0s, DNS look up: 0.002136s, Connection: 0.003243s, Pretransfer: 0.484455s, First byte at: 0.801602s
[2026-04-03 22:44:01] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 04 Apr 2026 02:44:01 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-03 22:44:11] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:11] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2026-04-03 22:44:11] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] 13774 rows after translation; translated 13523 `uniprot_entry` IDs in column `id_organism_a` to 13523 `uniprot` IDs in column `id_organism_a`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-03 22:44:11] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:11] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-03 22:44:11] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:44:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:44:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:44:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-03 22:44:12] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.736834s from rest.uniprot.org (42 bytes/s); Redirect: 0s, DNS look up: 0.002006s, Connection: 0.002921s, Pretransfer: 0.461857s, First byte at: 0.736784s
[2026-04-03 22:44:12] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 04 Apr 2026 02:44:12 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-03 22:44:18] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:18] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2026-04-03 22:44:18] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] 13774 rows after translation; translated 13226 `uniprot_entry` IDs in column `id_organism_b` to 13226 `uniprot` IDs in column `id_organism_b`.
[2026-04-03 22:44:18] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-03 22:44:18] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:18] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-04-03 22:44:18] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-03 22:44:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:44:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:44:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:44:19] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-03 22:44:19] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.487003s from rest.uniprot.org (88 bytes/s); Redirect: 0s, DNS look up: 0.00164s, Connection: 0.002399s, Pretransfer: 0.22069s, First byte at: 0.486934s
[2026-04-03 22:44:19] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 04 Apr 2026 02:44:19 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-03 22:44:25] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-04-03 22:44:25] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2026-04-03 22:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:25] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2026-04-03 22:44:25] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-04-03 22:44:25] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-03 22:44:25] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-03 22:44:25] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-03 22:44:25] [TRACE] [OmnipathR] 163601 rows before translation, 12830 uniprot IDs in column `uniprot`.
[2026-04-03 22:44:25] [TRACE] [OmnipathR] 163601 rows after translation; translated 12830 `uniprot` IDs in column `uniprot` to 12748 `genesymbol` IDs in column `genesymbol`.
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:44:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:44:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:44:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.362072s from omnipathdb.org (43.4 Kb/s); Redirect: 0s, DNS look up: 0.002187s, Connection: 0.002907s, Pretransfer: 0.208302s, First byte at: 0.361658s
[2026-04-03 22:44:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:44:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:44:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:44:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:30] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:44:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-03 22:44:32] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-03 22:44:32] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2026-04-03 22:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:32] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2026-04-03 22:44:40] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Organism(s): 10090
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:44:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:44:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:44:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:44:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.530991s from omnipathdb.org (29.6 Kb/s); Redirect: 0s, DNS look up: 0.002475s, Connection: 0.003088s, Pretransfer: 0.376017s, First byte at: 0.5302s
[2026-04-03 22:44:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:44:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:44:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:44:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-03 22:44:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:56] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:44:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-03 22:44:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-03 22:44:57] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2026-04-03 22:44:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:44:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:44:57] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2026-04-03 22:45:05] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2026-04-03 22:45:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:45:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:45:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:45:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:45:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.346441s from omnipathdb.org (45.3 Kb/s); Redirect: 0s, DNS look up: 0.001891s, Connection: 0.002687s, Pretransfer: 0.19755s, First byte at: 0.345459s
[2026-04-03 22:45:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:45:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:45:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:45:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:18] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:45:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-03 22:45:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-03 22:45:18] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-04-03 22:45:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:18] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-04-03 22:45:21] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-04-03 22:45:21] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:45:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-03 22:45:21] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:45:21] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:45:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:45:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-03 22:45:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-03 22:45:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-03 22:45:22] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.283677s from omnipathdb.org (23.7 Kb/s); Redirect: 0s, DNS look up: 0.00199s, Connection: 0.00271s, Pretransfer: 0.205848s, First byte at: 0.283392s
[2026-04-03 22:45:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 04 Apr 2026 02:45:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 04 Apr 2026 03:45:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-03 22:45:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:24] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-03 22:45:24] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-03 22:45:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:24] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-03 22:45:24] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-03 22:45:24] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-03 22:45:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-03 22:45:27] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-04-03 22:45:27] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-03 22:45:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-03 22:45:27] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-03 22:45:27] [TRACE] [OmnipathR] Orthology targets:
[2026-04-03 22:45:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-03 22:45:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-03 22:45:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-03 22:45:28] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-03 22:45:28] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-03 22:45:28] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-03 22:45:28] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-03 22:45:29] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
186.973 20.032 257.814
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.077 | 0.014 | 0.090 | |
| convert_f_defaults | 0.058 | 0.002 | 0.060 | |
| decouple | 0.001 | 0.000 | 0.000 | |
| dot-fit_preprocessing | 0.024 | 0.000 | 0.024 | |
| extract_sets | 0.025 | 0.000 | 0.025 | |
| filt_minsize | 0.042 | 0.001 | 0.043 | |
| get_collectri | 30.818 | 2.698 | 40.031 | |
| get_dorothea | 23.099 | 1.302 | 26.017 | |
| get_profile_of | 0.001 | 0.000 | 0.001 | |
| get_progeny | 7.394 | 0.877 | 14.329 | |
| get_resource | 1.191 | 0.347 | 3.514 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.028 | 0.005 | 0.033 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.039 | 0.006 | 0.044 | |
| run_aucell | 9.119 | 2.418 | 11.457 | |
| run_consensus | 1.858 | 0.443 | 2.283 | |
| run_fgsea | 23.178 | 0.797 | 23.943 | |
| run_gsva | 1.952 | 0.470 | 2.409 | |
| run_mdt | 0.145 | 0.025 | 0.164 | |
| run_mlm | 0.099 | 0.007 | 0.104 | |
| run_ora | 0.513 | 0.047 | 0.556 | |
| run_udt | 0.277 | 0.031 | 0.304 | |
| run_ulm | 0.076 | 0.007 | 0.083 | |
| run_viper | 0.770 | 0.183 | 0.946 | |
| run_wmean | 0.675 | 0.040 | 0.709 | |
| run_wsum | 0.689 | 0.052 | 0.735 | |
| show_methods | 0.053 | 0.000 | 0.052 | |
| show_resources | 0.198 | 0.018 | 1.012 | |
| tidyeval | 0 | 0 | 0 | |